Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects

Abstract

More than 190 plastid genomes have been completely sequenced during the past two decades due to advances in DNA sequencing technologies. Based on this unprecedented abundance of data, extensive genomic changes have been revealed in the plastid genomes. Inversion is the most common mechanism that leads to gene order changes. Several inversion events have been recognized as informative phylogenetic markers, such as a 30-kb inversion found in all living vascular plants minus lycopsids and two short inversions putatively shared by all ferns. Gene loss is a common event throughout plastid genome evolution. Many genes were independently lost or transferred to the nuclear genome in multiple plant lineages. The trnR-CCG gene was lost in some clades of lycophytes, ferns, and seed plants, and all the ndh genes were absent in parasitic plants, gnetophytes, Pinaceae, and the Taiwan moth orchid. Certain parasitic plants have, in particular, lost plastid genes related to photosynthesis because of the relaxation of functional constraint. The dramatic growth of plastid genome sequences has also promoted the use of whole plastid sequences and genomic features to solve phylogenetic problems. Chloroplast phylogenomics has provided additional evidence for deep-level phylogenetic relationships as well as increased phylogenetic resolutions at low taxonomic levels. However, chloroplast phylogenomics is still in its infant stage and rigorous analysis methodology has yet to be developed. Key words chloroplast phylogenomics, comparative genomics, gene loss, genome rearrangement, plastid genome sequencing.Plastid genome (plastome) sequence information is of central importance to tracing the evolutionary history of plastids and their hosts. The small genome size and high copy number per cell have made the plastid genomes much more amenable for sequencing than nuclear genomes. Currently, there are at least 190 completely sequenced plastid genomes available, of them 163 are from various green plants, with land plants having the best representation (137) (Fig. 1). Comparative studies indicate that plastid genomes have experienced substantial rearrangements and frequent gene losses throughout plant evolution. Some genes or groups of functionally related genes have been independently lost multiple times. These plastid genomic characters have been recognized as phylogentically informative markers. Based on the complete plastid genome sequence data, chloroplast phylogenomics has emerged as an effective approach to clarifying phylogenetic relationships in plants and algae.

Phylotranscriptomic analysis of the origin and early diversification of land plants

“…Whereas the monophyly of each bryophyte lineage-Bryophyta (mosses), Anthocerotophyta (hornworts), and Marchantiophyta (liverworts)-is strongly supported here (Figs. 2-4), most of our results reject the current, widely accepted hypothesis that liverworts are sister to all other land plants (38,42,71). Furthermore, the widely accepted view that liverworts, mosses, and hornworts are, respectively, successive sister groups to vascular plants (25,42,43)-which is strongly supported by parsimony mapping of mitochondrial intron gains (42) and recent mitochondrial phylogenomic analyses (72)-is not recovered in any of our analyses.…”

“…71). Bryophytes are resolved as monophyletic in several analyses here, including 3 of 12 amino acid supermatrix analyses and all ASTRAL analyses based on either amino acid data or in-frame nucleotide data without the inclusion of third positions (Figs.…”

Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research

“…Although six diverse chloroplast genomes of more than 190 completely sequenced plastid genomes (Gao et al, 2010) were selected to identify conserved regions of chloroplast genomes, it was necessary to test the effectiveness of these primer pairs with additional plant accessions. Castillo et al (2010) successfully transferred the use of SSR markers in barley to different species and genera.…”

“…However, the number of publicly announced whole genome sequences of higher plants or crop species remains extremely limited (Gao et al, 2010). Although conducting whole genome sequencing for each species or individuals can provide sufficient and accurate information, a significant amount of time and funding is required.…”

Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes

“…nuclear, mitochondrial and chloroplast ) support hornworts basal topology. Apart from the unresolved relationship of earliest land plants, another dilemma is represented by the controversy over paraphyletic Renzaglia et al 2000;Qiu et al 2006;Gao et al 2010) or monophyletic (Garbary et al 1993;Renzaglia and Garbary 2001;Nishiyama et al 2004) origin of bryophytes.…”